Testing statistical significance scores of sequence comparison methods with structure similarity

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Hulsen, Tim ^a   de Vlieg, Jacob ^a,b   Leunissen, Jack A M ^c   Groenen, Peter M A ^b  

^a RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^b Molecular Design and Informatics   (Netherlands)

^c WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

DATABASE SEARCHES; PROTEIN SEQUENCES; SEQUENCE COMPARISONS; STATISTICAL SIGNIFICANCE; STATISTICAL SIGNIFICANCE TEST; STATISTICAL VALIDATION; STRUCTURAL SIMILARITY; STRUCTURE SIMILARITY;

ALGORITHMS; DATABASE SYSTEMS; INFORMATION RETRIEVAL; PROTEINS; SEARCH ENGINES;

STATISTICS;

PROGESTERONE RECEPTOR; PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; HUMAN; INTERMETHOD COMPARISON; MONTE CARLO METHOD; NONHUMAN; PROTEIN DATABASE; PROTEIN STRUCTURE; RECEIVER OPERATING CHARACTERISTIC; SCORING SYSTEM; SIMULATION; STATISTICAL SIGNIFICANCE; VALIDATION PROCESS; COMPARATIVE STUDY; GENETICS; NUCLEOTIDE SEQUENCE; PROCEDURES; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; STATISTICS AND NUMERICAL DATA; STRUCTURAL HOMOLOGY;

BASE SEQUENCE; DATABASES, PROTEIN; HUMANS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 33750369354     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-444     Document Type: Article

References (32)

1. Smith TF, Waterman MS: Identification of common molecular subsequences. J Mol Biol 1981, 147(1):195-197.
2. Brenner SE, Chothia C, Hubbard TJ: Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc Natl Acad Sci U S A 1998, 95(11):6073-6078.
3. Pearson WR, Lipman DJ: Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A 1988, 85(8):2444-2448.
4. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402.
5. Paracel [http://www.paracel.com]
6. Pearson WR: Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics 1991, 11(3):635-650.
7. Rognes T: ParAlign: a parallel sequence alignment algorithm for rapid and sensitive database searches. Nucleic Acids Res 2001, 29(7):1647-1652.
8. Pearson WR, Sierk ML: The limits of protein sequence comparison? Curr Opin Struct Biol 2005.
9. Doolittle RF: Of URFs and ORFs: a primer on how to analyze derived amino acid sequences. Mill Valley California, University Science Books; 1986.
10. Gene-IT [http://www.gene-it.com]
11. Codani JJ, Comet JP, Aude JC, Glémet E, Wozniak A, Risler JL, Hénaut A, Slonimski PP: Automatic Analysis of Large-Scale Pairwise Alignments of Protein Sequences. Methods in Microbiology 1999, 28:229-244.
12. Kriventseva EV, Servant F, Apweiler R: Improvements to CluSTr: the database of SWISS-PR0T+TrEMBL protein clusters. Nucleic Acids Res 2003, 31(1):388-389.
13. Protein World [http://www.cmbi.ru.nl/pw/]
14. Hulsen T, Huynen MA, de Vlieg J, Groenen PM: Benchmarking ortholog identification methods using functional genomics data. Genome Biol 2006, 7(4):R31.
15. Booth HS, Maindonald JH, Wilson SR, Gready JE: An efficient Z-score algorithm for assessing sequence alignments. J Comput Biol 2004, 11(4):616-625.
16. Comet JP, Aude JC, Glemet E, Risler JL, Henaut A, Slonimski PP, Codani JJ: Significance of Z-value statistics of Smith-Waterman scores for protein alignments. Comput Chem 1999, 23(34):317-331.
17. Bastien O, Aude JC, Roy S, Marechal E: Fundamentals of massive automatic pairwise alignments of protein sequences: theoretical significance of Z-value statistics. Bioinformatics 2004, 20(4):534-537.
18. Chen Z: Assessing sequence comparison methods with the average precision criterion. Bioinformatics 2003, 19(18):2456-2460.
19. Gribskov M, Robinson NL: Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching. Compu Chem 1996, 20:25-33.
20. Kester AD, Buntinx F: Meta-analysis of ROC curves. Med Decis Making 2000, 20(4):430-439.
21. Schaffer AA, Aravind L, Madden TL, Shavirin S, Spouge JL, Wolf Yl, Koonin EV, Altschul SF: Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res 2001, 29(14):2994-3005.
22. Salton G: Developments in automatic text retrieval. Science 1991, 253:974-980.
23. Brenner SE, Koehl P, Levitt M: The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Res 2000, 28(1):254-256.
24. Park J, Karplus K, Barrett C, Hughey P. Haussler D, Hubbard T, Chothia C: Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J Mol Biol 1998, 284(4):1201-1210.
25. ASTRAL SCOP release 1.65 [http://astral.berkeley.edu/scopseq.1.65.html]
26. Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS: UniProt: the Universal Protein knowledgebase. Nucleic Acids Res 2004, 32(Database issue):D 115-9.
27. Agarwal P, States DJ: Comparative accuracy of methods for protein sequence similarity search. Bioinformatics 1998, 14(1):40-47.
28. Pearson WR: Comparison of methods for searching protein sequence databases. Protein Sci 1995, 4(6):1145-1160.
29. Henikoff S, Henikoff JG: Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A 1992, 89(22):10915-10919.
30. Reese JT, Pearson WR: Empirical determination of effective gap penalties for sequence comparison. Bioinformatics 2002, 18(11):1500-1507.
31. Price GA, Crooks GE, Green RE, Brenner SE: Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap. Bioinformatics 2005, 21(20):3824-3831.
32. Supplementary data [http://www.cmbi.ru.nl/~timhulse/ezcomp/]